Dynamic Aspects of Nucleic Acid-Protein Recognition

核酸-蛋白质识别的动态方面

• 批准号: 8064410
• 负责人: GARY Peter DROBNY
• 金额: $ 37.29万
• 依托单位: UNIVERSITY OF WASHINGTON
• 依托单位国家: 美国
• 财政年份: 1999
• 资助国家: 美国
• 起止时间: 1999-02-01 至 2013-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8064410
• 关键词: Adenine; Binding; Biological Process; Characteristics; Chemicals; Complex; Computer Simulation; Cytosine; DNA; DNA Methylation; DNA Sequence; Deoxycytidine; Development; Down-Regulation; Elements; Enzymes; Funding; Gene Expression Regulation; Genes; Goals; Health; HhaI methylase; Ligands; Link; Magic; Malignant Neoplasms; Measures; Messenger RNA; Methods; Methyltransferase; Molecular Models; Motion; Nucleic Acids; Open Reading Frames; Pathway interactions; Pattern; Play; Potential Energy; Process; Property; Proteins; RNA; Relaxation; Residual state; Resolution; Role; Solutions; Structure; Surface; Techniques; Time; Untranslated Regions; Up-Regulation; Work; base; conformational conversion; flexibility; genetic element; molecular dynamics; molecular modeling; mutant; programs; research study; response; solid solution; solid state; solid state nuclear magnetic resonance

DESCRIPTION (provided by applicant): We propose to describe the conformational transitions of paradigmatic nucleic acid complexes by using the results of solid state and solution NMR experiments to constrain long time scale computational simulations. In the previous funding period, we have demonstrated that solution and solid state NMR combined can cover motional processes that are not accessible to either technique separately, and have developed a formalism to extract the potential energy surface upon which dynamics occurs. We will apply these methods to describe at atomic resolution the sequence-specific conformational changes that occur in DNA as a methylase extrudes a base from the double helix. We will use the same methods in conjunction with real-time NMR methods to describe the conformational changes in a riboswitch at atomic resolution. We propose to study: I. The extrusion of a deoxycytidine from the double helix during DNA methylation - Using solid state and solution NMR methods together, we have observed unique motions within the target sequence for HhaI methylase. We hypothesize that these motions are specific to the GCGC repeat recognized by this enzyme and are important for base extrusion. II. The ligand-induced conformational changes in RNA - Riboswitches are genetic elements within the untranslated regions of mRNAs that regulate expression of certain enzymes. Direct binding of small metabolites to these RNAs alter their structures leading to up- or down-regulation of downstream open reading frames. PUBLIC HEALTH RELEVANCE: The enzymatic methylation of DNA is essential for many biological processes, and abnormal patterns of DNA methylation is characteristic of many cancers. Riboswitches are RNA elements capable of directly regulating biosynthetic pathways in response to changing levels of particular metabolites, and are able to couple metabolite recognition with gene regulation in the complete absence of protein helpers. We seek to better understand the functional impact of structural flexibility in DNA methylation and in the functioning of riboswitches.

描述(申请人提供)：我们建议使用固体和溶液核磁共振实验的结果来描述聚合核酸络合物的构象转变，以约束长时间尺度的计算模拟。在之前的资助期间，我们已经证明了溶液和固态核磁共振相结合可以涵盖任何一种技术都无法单独访问的运动过程，并开发了一种形式化方法来提取发生动力学的势能面。我们将应用这些方法来描述在原子分辨率下，当甲基酶从双螺旋中挤出碱基时DNA中发生的序列特有的构象变化。我们将使用相同的方法结合实时核磁共振方法来描述原子分辨率下核糖开关的构象变化。我们打算研究：1.DNA甲基化过程中脱氧胞苷从双螺旋中排出--结合使用固态和溶液核磁共振方法，我们观察到HHAI甲基酶在靶序列中的独特运动。我们假设这些运动是该酶识别的GCGC重复序列所特有的，并且对碱基挤出很重要。配体诱导的RNA-RiBoswitch的构象变化是位于mRNAs的非翻译区内的遗传元件，调节某些酶的表达。小的代谢物与这些RNA的直接结合改变了它们的结构，导致下游开放阅读框架的上调或下调。与公共卫生相关：DNA的酶催化甲基化对许多生物过程是必不可少的，而DNA甲基化的异常模式是许多癌症的特征。核糖开关是一种RNA元件，能够直接调节生物合成途径，以响应特定代谢物水平的变化，并能够在完全没有蛋白质辅助的情况下将代谢物识别与基因调控结合起来。我们试图更好地理解DNA甲基化和核糖开关功能中结构灵活性的功能影响。

项目成果

Monitoring tat peptide binding to TAR RNA by solid-state 31P-19F REDOR NMR.

• DOI: 10.1093/nar/gki626
• 发表时间: 2005
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Olsen GL;Edwards TE;Deka P;Varani G;Sigurdsson ST;Drobny GP
• 通讯作者: Drobny GP

Base Dynamics in the HhaI Protein Binding Site.

• DOI: 10.1021/acs.jpcb.3c03687
• 发表时间: 2023-08-24
• 期刊: JOURNAL OF PHYSICAL CHEMISTRY B
• 影响因子: 3.3
• 作者: Pederson, Kari;Meints, Gary A.;Drobny, Gary P.
• 通讯作者: Drobny, Gary P.

Preparation of RNA samples with narrow line widths for solid state NMR investigations.

• DOI: 10.1016/j.jmr.2012.07.018
• 发表时间: 2012-10
• 期刊: Journal of magnetic resonance
• 影响因子: 2.2
• 作者: Wei Huang;M. F. Bardaro;G. Varani;G. Drobny

13C/15N-19F intermolecular REDOR NMR study of the interaction of TAR RNA with Tat peptides.

• DOI: 10.1021/ja1051439
• 发表时间: 2010-12-22
• 期刊: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
• 影响因子: 15
• 作者: Huang, Wei;Varani, Gabriele;Drobny, Gary P.
• 通讯作者: Drobny, Gary P.

Intermediate rate atomic trajectories of RNA by solid-state NMR spectroscopy.

• DOI: 10.1021/ja907515s
• 发表时间: 2010-01-13
• 期刊: JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
• 影响因子: 15
• 作者: Olsen, Greg L.;Bardaro, Michael F., Jr.;Echodu, Dorothy C.;Drobny, Gary P.;Varani, Gabriele
• 通讯作者: Varani, Gabriele